RunCoNGA: Run CoNGA

In bimberlabinternal/CellMembrane: A package with high-level wrappers and pipelines for single-cell RNA-seq tools

Run CoNGA

Description

Runs CoNGA on a seurat object

Usage

RunCoNGA(
  seuratObj = NULL,
  tcrClonesFile = NULL,
  seuratToCongaDir = "./seuratToConga",
  assayName = "RNA",
  organism = NULL,
  runCongaOutputFilePrefix = "conga_output",
  gexDatatype = "10x_h5",
  runCongaOutfilePrefixForQcPlots = "qc_plots",
  runCongaOutputDirectory = "./conga_output",
  congaMetadataPrefix = "conga_",
  pngConversionTool = NULL
)

Arguments

seuratObj	The Seurat object containing the data to be run using CoNGA.
tcrClonesFile	The 10x clonotypes file for this Seurat object. Single lanes can use the CellRanger/Vloupe contigs CSV file. Merged lanes need to merge these files and modify them to create unique cellbarcodes and clonotype names, such as the code from Rdiscvr::CreateMergedTcrClonotypeFile().
seuratToCongaDir	The directory to store the results of SeuratToCoNGA() (the input files for the python call to run_CoNGA()).
assayName	Pass-through variable for accessing the assay name within the Seurat object for SeuratToCoNGA().
organism	'human' or 'rhesus'
runCongaOutputFilePrefix	prefix for the output files from the python call to run_CoNGA().
gexDatatype	This should be "10x_h5" since we're using DropletUtils to write the counts, although "h5ad" is supported.
runCongaOutfilePrefixForQcPlots	Prefix for the qc output files to be generated by run_CoNGA().
runCongaOutputDirectory	The directory that will store the many files created during run_CoNGA().
congaMetadataPrefix	A prefix to be added to the columns of the metadata that will be added from CoNGA within the returned Seurat object.
pngConversionTool	specify the conversion tool used by CoNGA for svg to png conversion. Can be any of: convert, inkscape, rsvg

Value

A Seurat object with the conga metadata relevant to TCR + gene expression clustering appended.

Examples

## Not run: 
  CreateMergedTcrClonotypeFile(seuratObj,
                               outputFile = "./tcrs.csv")
  congaSeuratObj <- RunCoNGA(seuratObj = seuratObj,
                             tcrClonesFile = "./tcrs.csv",
                             organism = "rhesus")

## End(Not run)

bimberlabinternal/CellMembrane documentation built on Dec. 25, 2024, 8:10 a.m.